Example usage for org.springframework.batch.core JobExecution getExitStatus

List of usage examples for org.springframework.batch.core JobExecution getExitStatus

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Introduction

In this page you can find the example usage for org.springframework.batch.core JobExecution getExitStatus.

Prototype

public ExitStatus getExitStatus()

Source Link

Usage

From source file:uk.ac.ebi.eva.pipeline.jobs.steps.VariantLoaderStepTest.java

@Test
public void loaderStepShouldLoadAllVariants() throws Exception {
    Config.setOpenCGAHome(opencgaHome);//ww  w . j a  v  a2 s .co m

    jobOptions.getVariantOptions().put(VariantStorageManager.DB_NAME, dbName);
    jobOptions.getVariantOptions().put(VARIANT_SOURCE, new VariantSource(input, "1", "1", "studyName",
            VariantStudy.StudyType.COLLECTION, VariantSource.Aggregation.NONE));

    //and a variants transform step already executed
    File transformedVcfVariantsFile = new File(
            VariantLoaderStepTest.class.getResource("/small20.vcf.gz.variants.json.gz").getFile());
    File tmpTransformedVcfVariantsFile = new File(outputDir, transformedVcfVariantsFile.getName());
    FileUtils.copyFile(transformedVcfVariantsFile, tmpTransformedVcfVariantsFile);

    File transformedVariantsFile = new File(
            VariantLoaderStepTest.class.getResource("/small20.vcf.gz.file.json.gz").getFile());
    File tmpTransformedVariantsFile = new File(outputDir, transformedVariantsFile.getName());
    FileUtils.copyFile(transformedVariantsFile, tmpTransformedVariantsFile);

    // When the execute method in variantsLoad is executed
    JobExecution jobExecution = jobLauncherTestUtils.launchStep(GenotypedVcfJob.LOAD_VARIANTS);

    //Then variantsLoad step should complete correctly
    assertEquals(ExitStatus.COMPLETED, jobExecution.getExitStatus());
    assertEquals(BatchStatus.COMPLETED, jobExecution.getStatus());

    // And the number of documents in db should be the same number of line of the vcf transformed file
    VariantStorageManager variantStorageManager = StorageManagerFactory.getVariantStorageManager();
    VariantDBAdaptor variantDBAdaptor = variantStorageManager.getDBAdaptor(dbName, null);
    VariantDBIterator iterator = variantDBAdaptor.iterator(new QueryOptions());
    long lines = getLines(new GZIPInputStream(new FileInputStream(transformedVcfVariantsFile)));

    assertEquals(count(iterator), lines);

    tmpTransformedVcfVariantsFile.delete();
    tmpTransformedVariantsFile.delete();
}

From source file:uk.ac.ebi.eva.pipeline.jobs.steps.PopulationStatisticsGeneratorStepTest.java

@Test
public void statisticsGeneratorStepShouldCalculateStats() throws IOException, InterruptedException {
    //and a valid variants load step already completed
    String dump = PopulationStatisticsGeneratorStepTest.class.getResource("/dump/").getFile();
    restoreMongoDbFromDump(dump);//from w  ww. j  a  v a2 s  .co  m

    //Given a valid VCF input file
    String input = SMALL_VCF_FILE;

    pipelineOptions.put("input.vcf", input);
    variantOptions.put(VariantStorageManager.DB_NAME, STATS_DB);

    VariantSource source = new VariantSource(input, "1", "1", "studyName", VariantStudy.StudyType.COLLECTION,
            VariantSource.Aggregation.NONE);

    variantOptions.put(VARIANT_SOURCE, source);

    statsFile = new File(Paths.get(pipelineOptions.getString("output.dir.statistics"))
            .resolve(VariantStorageManager.buildFilename(source)) + ".variants.stats.json.gz");
    statsFile.delete();
    assertFalse(statsFile.exists()); // ensure the stats file doesn't exist from previous executions

    // When the execute method in variantsStatsCreate is executed
    JobExecution jobExecution = jobLauncherTestUtils.launchStep(PopulationStatisticsJob.CALCULATE_STATISTICS);

    //Then variantsStatsCreate step should complete correctly
    assertEquals(ExitStatus.COMPLETED, jobExecution.getExitStatus());
    assertEquals(BatchStatus.COMPLETED, jobExecution.getStatus());

    //and the file containing statistics should exist
    assertTrue(statsFile.exists());

    //delete created files
    statsFile.delete();
    new File(Paths.get(pipelineOptions.getString("output.dir.statistics"))
            .resolve(VariantStorageManager.buildFilename(source)) + ".source.stats.json.gz").delete();

}

From source file:uk.ac.ebi.eva.pipeline.jobs.GenotypedVcfJobWorkflowTest.java

@Test
public void optionalStepsShouldBeSkipped() throws Exception {
    initVariantConfigurationJob();//w w w .ja  v a 2 s.  c om

    jobOptions.getPipelineOptions().put(AnnotationJob.SKIP_ANNOT, true);
    jobOptions.getPipelineOptions().put(PopulationStatisticsJob.SKIP_STATS, true);

    JobExecution execution = jobLauncherTestUtils.launchJob();

    assertEquals(ExitStatus.COMPLETED, execution.getExitStatus());
    assertEquals(2, execution.getStepExecutions().size());

    List<StepExecution> steps = new ArrayList<>(execution.getStepExecutions());
    StepExecution transformStep = steps.get(0);
    StepExecution loadStep = steps.get(1);

    assertEquals(GenotypedVcfJob.NORMALIZE_VARIANTS, transformStep.getStepName());
    assertEquals(GenotypedVcfJob.LOAD_VARIANTS, loadStep.getStepName());

    assertTrue(transformStep.getEndTime().before(loadStep.getStartTime()));
}

From source file:uk.ac.ebi.eva.pipeline.jobs.steps.VariantLoaderStepTest.java

@Test
public void loaderStepShouldFailBecauseOpenCGAHomeIsWrong() throws JobExecutionException {
    String inputFile = VariantLoaderStepTest.class.getResource(input).getFile();

    Config.setOpenCGAHome("");

    jobOptions.getPipelineOptions().put("input.vcf", inputFile);
    jobOptions.getVariantOptions().put(VariantStorageManager.DB_NAME, dbName);

    VariantSource source = (VariantSource) jobOptions.getVariantOptions()
            .get(VariantStorageManager.VARIANT_SOURCE);

    jobOptions.getVariantOptions().put(VariantStorageManager.VARIANT_SOURCE,
            new VariantSource(input, source.getFileId(), source.getStudyId(), source.getStudyName(),
                    source.getType(), source.getAggregation()));

    JobExecution jobExecution = jobLauncherTestUtils.launchStep(GenotypedVcfJob.LOAD_VARIANTS);

    assertEquals(inputFile, jobOptions.getPipelineOptions().getString("input.vcf"));
    assertEquals(ExitStatus.FAILED.getExitCode(), jobExecution.getExitStatus().getExitCode());
}

From source file:uk.ac.ebi.eva.pipeline.jobs.GenotypedVcfJobWorkflowTest.java

@Test
public void annotationStepsShouldBeSkipped() throws Exception {
    initVariantConfigurationJob();/*from  w  w w.j ava  2  s .  c o m*/
    jobOptions.getPipelineOptions().put(AnnotationJob.SKIP_ANNOT, true);

    JobExecution execution = jobLauncherTestUtils.launchJob();

    assertEquals(ExitStatus.COMPLETED, execution.getExitStatus());
    assertEquals(4, execution.getStepExecutions().size());

    List<StepExecution> steps = new ArrayList<>(execution.getStepExecutions());
    StepExecution transformStep = steps.get(0);
    StepExecution loadStep = steps.get(1);

    Map<String, StepExecution> parallelStepsNameToStepExecution = new HashMap<>();
    for (int i = 2; i <= steps.size() - 1; i++) {
        parallelStepsNameToStepExecution.put(steps.get(i).getStepName(), steps.get(i));
    }

    assertEquals(GenotypedVcfJob.NORMALIZE_VARIANTS, transformStep.getStepName());
    assertEquals(GenotypedVcfJob.LOAD_VARIANTS, loadStep.getStepName());

    Set<String> parallelStepNamesExecuted = parallelStepsNameToStepExecution.keySet();
    Set<String> parallelStepNamesToCheck = new HashSet<>(Arrays
            .asList(PopulationStatisticsJob.CALCULATE_STATISTICS, PopulationStatisticsJob.LOAD_STATISTICS));

    assertEquals(parallelStepNamesToCheck, parallelStepNamesExecuted);

    assertTrue(transformStep.getEndTime().before(loadStep.getStartTime()));
    assertTrue(loadStep.getEndTime().before(
            parallelStepsNameToStepExecution.get(PopulationStatisticsJob.CALCULATE_STATISTICS).getStartTime()));

    assertTrue(parallelStepsNameToStepExecution.get(PopulationStatisticsJob.CALCULATE_STATISTICS).getEndTime()
            .before(parallelStepsNameToStepExecution.get(PopulationStatisticsJob.LOAD_STATISTICS)
                    .getStartTime()));
}

From source file:uk.ac.ebi.eva.pipeline.jobs.GenotypedVcfJobWorkflowTest.java

@Test
public void statsStepsShouldBeSkipped() throws Exception {
    initVariantConfigurationJob();/*from ww  w .  j a va 2  s  .com*/
    jobOptions.getPipelineOptions().put(PopulationStatisticsJob.SKIP_STATS, true);

    jobOptions.getPipelineOptions().put("db.name", "diegoTest");

    JobExecution execution = jobLauncherTestUtils.launchJob();

    assertEquals(ExitStatus.COMPLETED, execution.getExitStatus());
    assertEquals(5, execution.getStepExecutions().size());

    List<StepExecution> steps = new ArrayList<>(execution.getStepExecutions());
    StepExecution transformStep = steps.get(0);
    StepExecution loadStep = steps.get(1);

    Map<String, StepExecution> parallelStepsNameToStepExecution = new HashMap<>();
    for (int i = 2; i <= steps.size() - 1; i++) {
        parallelStepsNameToStepExecution.put(steps.get(i).getStepName(), steps.get(i));
    }

    assertEquals(GenotypedVcfJob.NORMALIZE_VARIANTS, transformStep.getStepName());
    assertEquals(GenotypedVcfJob.LOAD_VARIANTS, loadStep.getStepName());

    Set<String> parallelStepNamesExecuted = parallelStepsNameToStepExecution.keySet();
    Set<String> parallelStepNamesToCheck = new HashSet<>(Arrays.asList(
            VepInputGeneratorStep.FIND_VARIANTS_TO_ANNOTATE, VepAnnotationGeneratorStep.GENERATE_VEP_ANNOTATION,
            AnnotationLoaderStep.LOAD_VEP_ANNOTATION));

    assertEquals(parallelStepNamesToCheck, parallelStepNamesExecuted);

    assertTrue(transformStep.getEndTime().before(loadStep.getStartTime()));
    assertTrue(loadStep.getEndTime().before(parallelStepsNameToStepExecution
            .get(VepInputGeneratorStep.FIND_VARIANTS_TO_ANNOTATE).getStartTime()));

    assertTrue(parallelStepsNameToStepExecution.get(VepInputGeneratorStep.FIND_VARIANTS_TO_ANNOTATE)
            .getEndTime().before(parallelStepsNameToStepExecution
                    .get(VepAnnotationGeneratorStep.GENERATE_VEP_ANNOTATION).getStartTime()));
    assertTrue(parallelStepsNameToStepExecution.get(VepAnnotationGeneratorStep.GENERATE_VEP_ANNOTATION)
            .getEndTime().before(parallelStepsNameToStepExecution.get(AnnotationLoaderStep.LOAD_VEP_ANNOTATION)
                    .getStartTime()));
}

From source file:uk.ac.ebi.eva.pipeline.jobs.GenotypedVcfJobWorkflowTest.java

@Test
public void allStepsShouldBeExecuted() throws Exception {
    initVariantConfigurationJob();/*w w w.j a  v a 2s .c  om*/

    JobExecution execution = jobLauncherTestUtils.launchJob();

    assertEquals(ExitStatus.COMPLETED, execution.getExitStatus());
    assertEquals(7, execution.getStepExecutions().size());

    List<StepExecution> steps = new ArrayList<>(execution.getStepExecutions());
    StepExecution transformStep = steps.get(0);
    StepExecution loadStep = steps.get(1);

    Map<String, StepExecution> parallelStepsNameToStepExecution = new HashMap<>();
    for (int i = 2; i <= steps.size() - 1; i++) {
        parallelStepsNameToStepExecution.put(steps.get(i).getStepName(), steps.get(i));
    }

    assertEquals(GenotypedVcfJob.NORMALIZE_VARIANTS, transformStep.getStepName());
    assertEquals(GenotypedVcfJob.LOAD_VARIANTS, loadStep.getStepName());

    Set<String> parallelStepNamesExecuted = parallelStepsNameToStepExecution.keySet();
    Set<String> parallelStepNamesToCheck = new HashSet<>(Arrays.asList(
            PopulationStatisticsJob.CALCULATE_STATISTICS, PopulationStatisticsJob.LOAD_STATISTICS,
            VepInputGeneratorStep.FIND_VARIANTS_TO_ANNOTATE, VepAnnotationGeneratorStep.GENERATE_VEP_ANNOTATION,
            AnnotationLoaderStep.LOAD_VEP_ANNOTATION));

    assertEquals(parallelStepNamesToCheck, parallelStepNamesExecuted);

    assertTrue(transformStep.getEndTime().before(loadStep.getStartTime()));
    assertTrue(loadStep.getEndTime().before(
            parallelStepsNameToStepExecution.get(PopulationStatisticsJob.CALCULATE_STATISTICS).getStartTime()));
    assertTrue(loadStep.getEndTime().before(parallelStepsNameToStepExecution
            .get(VepInputGeneratorStep.FIND_VARIANTS_TO_ANNOTATE).getStartTime()));

    assertTrue(parallelStepsNameToStepExecution.get(PopulationStatisticsJob.CALCULATE_STATISTICS).getEndTime()
            .before(parallelStepsNameToStepExecution.get(PopulationStatisticsJob.LOAD_STATISTICS)
                    .getStartTime()));
    assertTrue(parallelStepsNameToStepExecution.get(VepInputGeneratorStep.FIND_VARIANTS_TO_ANNOTATE)
            .getEndTime().before(parallelStepsNameToStepExecution
                    .get(VepAnnotationGeneratorStep.GENERATE_VEP_ANNOTATION).getStartTime()));
    assertTrue(parallelStepsNameToStepExecution.get(VepAnnotationGeneratorStep.GENERATE_VEP_ANNOTATION)
            .getEndTime().before(parallelStepsNameToStepExecution.get(AnnotationLoaderStep.LOAD_VEP_ANNOTATION)
                    .getStartTime()));
}

From source file:uk.ac.ebi.eva.pipeline.jobs.GenotypedVcfJobTest.java

@Test
public void fullGenotypedVcfJob() throws Exception {
    String inputFile = GenotypedVcfJobTest.class.getResource(input).getFile();
    String mockVep = GenotypedVcfJobTest.class.getResource("/mockvep.pl").getFile();

    jobOptions.getPipelineOptions().put("input.vcf", inputFile);
    jobOptions.getPipelineOptions().put("app.vep.path", mockVep);

    Config.setOpenCGAHome(opencgaHome);// ww  w  .j  av a 2  s.  c  o  m

    // transformedVcf file init
    String transformedVcf = outputDir + input + ".variants.json" + compressExtension;
    File transformedVcfFile = new File(transformedVcf);
    transformedVcfFile.delete();
    assertFalse(transformedVcfFile.exists());

    //stats file init
    VariantSource source = (VariantSource) jobOptions.getVariantOptions()
            .get(VariantStorageManager.VARIANT_SOURCE);
    File statsFile = new File(Paths.get(outputDir).resolve(VariantStorageManager.buildFilename(source))
            + ".variants.stats.json.gz");
    statsFile.delete();
    assertFalse(statsFile.exists()); // ensure the stats file doesn't exist from previous executions

    // annotation files init
    File vepInputFile = new File(vepInput);
    vepInputFile.delete();
    assertFalse(vepInputFile.exists());

    File vepOutputFile = new File(vepOutput);
    vepOutputFile.delete();
    assertFalse(vepOutputFile.exists());

    VariantDBIterator iterator;

    // Run the Job
    JobExecution jobExecution = jobLauncherTestUtils.launchJob();

    assertEquals(ExitStatus.COMPLETED, jobExecution.getExitStatus());
    assertEquals(BatchStatus.COMPLETED, jobExecution.getStatus());

    // 1 transform step: check transformed file
    long transformedLinesCount = getLines(new GZIPInputStream(new FileInputStream(transformedVcf)));
    assertEquals(300, transformedLinesCount);

    // 2 load step: check ((documents in DB) == (lines in transformed file))
    //variantStorageManager = StorageManagerFactory.getVariantStorageManager();
    //variantDBAdaptor = variantStorageManager.getDBAdaptor(dbName, null);
    iterator = getVariantDBIterator();
    assertEquals(transformedLinesCount, count(iterator));

    // 3 create stats step
    assertTrue(statsFile.exists());

    // 4 load stats step: check ((documents in DB) == (lines in transformed file))
    //variantStorageManager = StorageManagerFactory.getVariantStorageManager();
    //variantDBAdaptor = variantStorageManager.getDBAdaptor(dbName, null);
    iterator = getVariantDBIterator();
    assertEquals(transformedLinesCount, count(iterator));

    // check the DB docs have the field "st"
    iterator = getVariantDBIterator();

    assertEquals(1, iterator.next().getSourceEntries().values().iterator().next().getCohortStats().size());

    // 5 annotation flow
    // annotation input vep generate step
    BufferedReader testReader = new BufferedReader(new InputStreamReader(
            new FileInputStream(GenotypedVcfJobTest.class.getResource("/preannot.sorted").getFile())));
    BufferedReader actualReader = new BufferedReader(
            new InputStreamReader(new FileInputStream(vepInputFile.toString())));

    ArrayList<String> rows = new ArrayList<>();

    String s;
    while ((s = actualReader.readLine()) != null) {
        rows.add(s);
    }
    Collections.sort(rows);

    String testLine = testReader.readLine();
    for (String row : rows) {
        assertEquals(testLine, row);
        testLine = testReader.readLine();
    }
    assertNull(testLine); // if both files have the same length testReader should be after the last line

    // 6 annotation create step
    assertTrue(vepInputFile.exists());
    assertTrue(vepOutputFile.exists());

    // Check output file length
    assertEquals(537, getLines(new GZIPInputStream(new FileInputStream(vepOutput))));

    // 8 Annotation load step: check documents in DB have annotation (only consequence type)
    iterator = getVariantDBIterator();

    int cnt = 0;
    int consequenceTypeCount = 0;
    while (iterator.hasNext()) {
        cnt++;
        Variant next = iterator.next();
        if (next.getAnnotation().getConsequenceTypes() != null) {
            consequenceTypeCount += next.getAnnotation().getConsequenceTypes().size();
        }
    }

    assertEquals(300, cnt);
    assertEquals(536, consequenceTypeCount);

    //check that one line is skipped because malformed
    List<StepExecution> variantAnnotationLoadStepExecution = jobExecution.getStepExecutions().stream().filter(
            stepExecution -> stepExecution.getStepName().equals(AnnotationLoaderStep.LOAD_VEP_ANNOTATION))
            .collect(Collectors.toList());
    assertEquals(1, variantAnnotationLoadStepExecution.get(0).getReadSkipCount());

}

From source file:de.codecentric.batch.web.JobOperationsController.java

@RequestMapping(value = "/jobs/executions/{executionId}", method = RequestMethod.GET)
public String getStatus(@PathVariable long executionId) throws NoSuchJobExecutionException {
    if (LOG.isDebugEnabled()) {
        LOG.debug("Get ExitCode for JobExecution with id: " + executionId + ".");
    }//from w ww.  ja v a 2s . c o m
    JobExecution jobExecution = jobExplorer.getJobExecution(executionId);
    if (jobExecution != null) {
        return jobExecution.getExitStatus().getExitCode();
    } else {
        throw new NoSuchJobExecutionException("JobExecution with id " + executionId + " not found.");
    }
}

From source file:com.github.jrrdev.mantisbtsync.core.jobs.issues.tasklets.IssuesLastRunExtractorTasklet.java

/**
 * {@inheritDoc}//  ww w. j  av a 2  s  .  c o  m
 * @see org.springframework.batch.core.step.tasklet.Tasklet#execute(org.springframework.batch.core.StepContribution, org.springframework.batch.core.scope.context.ChunkContext)
 */
@Override
public RepeatStatus execute(final StepContribution contribution, final ChunkContext chunkContext)
        throws Exception {

    final StepContext stepContext = chunkContext.getStepContext();
    final String jobName = stepContext.getJobName();
    final JobParameters jobParams = stepContext.getStepExecution().getJobParameters();
    final Map<String, JobParameter> currParams = new HashMap<String, JobParameter>(jobParams.getParameters());
    currParams.remove("run.id");

    Date lastJobRun = null;

    final List<JobInstance> jobInstances = jobExplorer.getJobInstances(jobName, 0, 1000);
    for (final JobInstance jobInstance : jobInstances) {
        final List<JobExecution> jobExecutions = jobExplorer.getJobExecutions(jobInstance);
        for (final JobExecution jobExecution : jobExecutions) {

            final JobParameters oldJobParams = jobExecution.getJobParameters();
            final Map<String, JobParameter> oldParams = new HashMap<String, JobParameter>(
                    oldJobParams.getParameters());
            oldParams.remove("run.id");

            if (ExitStatus.COMPLETED.equals(jobExecution.getExitStatus()) && oldParams.equals(currParams)) {

                if (lastJobRun == null || lastJobRun.before(jobExecution.getStartTime())) {
                    lastJobRun = jobExecution.getStartTime();
                }
            }
        }
    }

    if (lastJobRun != null) {
        stepContext.getStepExecution().getExecutionContext().put("mantis.update.last_job_run", lastJobRun);
    }

    stepContext.getStepExecution().getExecutionContext().put("mantis.update.current_job_run",
            Calendar.getInstance());

    return RepeatStatus.FINISHED;
}